Comment # 5 on bug 1216040 from Dr. Werner Fink

(In reply to Antonios Konstantinos Pappas from comment #3)
> Deleting the cache does not resolve the issue. Unless using spacemacs and
> probably other distributions is not a supported use case, I would suggest
> this is a bug.

You have run

   rm -rf /home/apappas/.emacs.d/eln-cache/*

have you ... or in emacs the command native-compile-prune-cache ?

(In reply to Antonios Konstantinos Pappas from comment #4)
> Created attachment 869998 [details]
> Output of  emacs --debug-init

First line of the log shows

  native-lisp-file-inconsistent

And what is

  /home/apappas/.emacs.d/init.el

for?